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Links from GEO DataSets

Items: 20

1.

An epigenetic signature of developmental potential in neural stem cells and early neurons [ChIP-seq]

(Submitter supplied) A cardinal property of neural stem cells (NSCs) is their ability to adopt multiple fates upon differentiation. The epigenome is widely seen as a read-out of cellular potential and a manifestation of this can be seen in embryonic stem cells (ESCs), where promoters of many lineage-specific regulators are marked by a bivalent epigenetic signature comprising trimethylation of both lysine 4 and lysine 27 of histone H3 (H3K4me3 and H3K27me3, respectively). more...
Organism:
Mus musculus
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL9185
6 Samples
Download data: BED, CSV
Series
Accession:
GSE46792
ID:
200046792
2.

An epigenetic signature of developmental potential in neural stem cells and early neurons

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Mus musculus
Type:
Expression profiling by array; Genome binding/occupancy profiling by high throughput sequencing
Platforms:
GPL9185 GPL6885
14 Samples
Download data: BED, CSV
Series
Accession:
GSE46793
ID:
200046793
3.

An epigenetic signature of developmental potential in neural stem cells and early neurons [expression]

(Submitter supplied) A cardinal property of neural stem cells (NSCs) is their ability to adopt multiple fates upon differentiation. The epigenome is widely seen as a read-out of cellular potential and a manifestation of this can be seen in embryonic stem cells (ESCs), where promoters of many lineage-specific regulators are marked by a bivalent epigenetic signature comprising trimethylation of both lysine 4 and lysine 27 of histone H3 (H3K4me3 and H3K27me3, respectively). more...
Organism:
Mus musculus
Type:
Expression profiling by array
Platform:
GPL6885
8 Samples
Download data: TXT
Series
Accession:
GSE46791
ID:
200046791
4.

ChIP-chip and MeDIP-chip from glioblastoma BTSCs (brain tumor stem cells) with H3K4me3, H3K27me3, H3K9me3, methylated DNA

(Submitter supplied) Aberrational epigenetic marks are believed to play a major role in establishing the abnormal features of cancer cells. Rational use and development of drugs aimed at epigenetic processes requires an understanding of the range, extent, and roles of epigenetic reprogramming in cancer cells. Using ChIP-chip and MeDIP-chip approaches, we localized well-established and prevalent epigenetic marks (H3K27me3, H3K4me3, H3K9me3, DNA methylation) on a genome scale in several lines of putative glioma stem cells (brain tumor stem cells, BTSCs) and, for comparison, normal human fetal neural stem cells (fNSCs). more...
Organism:
Homo sapiens
Type:
Genome binding/occupancy profiling by genome tiling array; Methylation profiling by genome tiling array
Platform:
GPL9464
20 Samples
Download data: GFF, PAIR
Series
Accession:
GSE60806
ID:
200060806
5.

Geminin regulates the transcriptional and epigenetic status of neuronal fate promoting genes during mammalian neurogenesis

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Xenopus laevis; Mus musculus
Type:
Expression profiling by high throughput sequencing; Expression profiling by array
Platforms:
GPL13112 GPL1318
10 Samples
Download data: CEL, TXT
Series
Accession:
GSE39673
ID:
200039673
6.

Regulation of neurogenin-dependent gene expression by geminin

(Submitter supplied) Transcriptional targets of neurogenin (Ngnr1) were identified by over-expression of an inducible form of neurogenin in Xenopus ectodermal explants. The effects of co-expressing the nucleoprotein geminin on Ngnr1-dependent target gene transactivation were defined. Regulating the transition from lineage-restricted progenitors to terminally differentiated cells is a central aspect of nervous system development. more...
Organism:
Xenopus laevis
Type:
Expression profiling by array
Platform:
GPL1318
6 Samples
Download data: CEL
Series
Accession:
GSE39658
ID:
200039658
7.

Geminin knockdown in embryonic stem cell-derived neural precursors

(Submitter supplied) Regulating the transition from lineage-restricted progenitors to terminally differentiated cells is a central aspect of nervous system development. Here, we investigated the role of the nucleoprotein Geminin in regulating neurogenesis at a mechanistic level during both Xenopus primary neurogenesis and mammalian neuronal differentiation in vitro. The latter work utilized both neural cells derived from embryonic stem and embryonal carcinoma cells in vitro and neural stem cells from mouse forebrain. more...
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL13112
4 Samples
Download data: TXT
Series
Accession:
GSE39657
ID:
200039657
8.

Human ES cell-derived neural rosettes reveal a functionally distinct early neural stem cell stage

(Submitter supplied) All data are derived from the same batch of human ES cells (line H9, WA-09). With the exception of the “UD” file all files represent neural cell types derived from the undifferentiated hESCs. Following mechanical isolation, rosettes were maintained for various passages in the presence of defined growth factors and morphogen factors as indicated below at the R-NSC stage. Cells at the NSCFGF/EGF stage were derived from mechanically isolated neural rosettes that were purified and long-term expanded as attached monolayer cultures in serum free medium in the presence of FGF2/EGF. more...
Organism:
Homo sapiens
Type:
Expression profiling by array
Platform:
GPL570
7 Samples
Download data: CHP
Series
Accession:
GSE9921
ID:
200009921
9.

Mll2 is required for H3K4 trimethylation on bivalent promoters in ES cells whereas Mll1 is redundant

(Submitter supplied) Trimethylation of histone 3 lysine 4 (H3K4me3) at promoters of actively transcribed genes is a universal epigenetic mark and a key product of Trithorax-Group action. Here we show that Mll2, one of the six Set1/Trithorax-type H3K4 methyltransferases in mammals, is required for trimethylation of bivalent promoters in mouse embryonic stem cells. Mll2 is bound to bivalent promoters but also to most active promoters, which do not require Mll2 for H3K4me3 or mRNA expression. more...
Organism:
Mus musculus
Type:
Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platforms:
GPL11002 GPL13112
30 Samples
Download data: BED, WIG
Series
Accession:
GSE52071
ID:
200052071
10.

Chromatin remodeling during in vivo neural stem cells differentiating to neurons in early Drosophila embryos

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Drosophila melanogaster
Type:
Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL13304
14 Samples
Download data: BED, BW, TXT
Series
Accession:
GSE80458
ID:
200080458
11.

Chromatin remodeling during in vivo neural stem cells differentiating to neurons in early Drosophila embryos [ChIP-seq]

(Submitter supplied) Chromatin profiling of affinity-purified nuclei of neural stem cells (NSCs) and neurons from the Drosophila embryos, respectively.
Organism:
Drosophila melanogaster
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL13304
12 Samples
Download data: BED, BW, TXT
Series
Accession:
GSE80457
ID:
200080457
12.

Chromatin remodeling during in vivo neural stem cells differentiating to neurons in early Drosophila embryos [RNA-seq]

(Submitter supplied) Expression profiles of affinity-purified nuclei of neural stem cells (NSCs) and neurons from the Drosophila embryos.
Organism:
Drosophila melanogaster
Type:
Expression profiling by high throughput sequencing
Platform:
GPL13304
2 Samples
Download data: TXT
Series
Accession:
GSE80456
ID:
200080456
13.

An epigenetic profile of early T-cell development from multipotent progenitors to committed T-cell descendants.

(Submitter supplied) Using a stromal cell free system, we described the gene expression and two genome wide epigenetic profiles of a unique population of undifferentiated bone marrow cells selectively driven towards the T cell differentiation pathway
Organism:
Mus musculus
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL11002
15 Samples
Download data: WIG
Series
Accession:
GSE47995
ID:
200047995
14.

An epigenetic profile of early T-cell development from multipotent progenitors to committed T-cell descendants.

(Submitter supplied) Using a stromal cell free system, we described the gene expression and two genome wide epigenetic profiles of a unique population of undifferentiated bone marrow cells selectively driven towards the T cell differentiation pathway
Organism:
Mus musculus
Type:
Expression profiling by array
Platform:
GPL6246
6 Samples
Download data: CEL
Series
Accession:
GSE47940
ID:
200047940
15.

Genome-wide Definition of Promoter and Enhancer Usage During Neural Induction of Human Embryonic Stem Cells

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by array
Platforms:
GPL19171 GPL10999
10 Samples
Download data: BED, CEL, TXT
Series
Accession:
GSE61267
ID:
200061267
16.

Genome-wide Definition of Promoter and Enhancer Usage During Neural Induction of Human Embryonic Stem Cells [gene expression profile]

(Submitter supplied) Genome-wide mapping of transcriptional regulatory elements are essential tools for the understanding of the molecular events orchestrating self-renewal, commitment and differentiation of stem cells. We combined high-throughput identification of nascent, Pol-II-transcribed RNAs by Cap Analysis of Gene Expression (CAGE-Seq) with genome-wide profiling of histones modifications by chromatin immunoprecipitation (ChIP-seq) to map active promoters and enhancers in a model of human neural commitment, represented by embryonic stem cells (ESCs) induced to differentiate into self-renewing neuroepithelial-like stem cells (NESC). more...
Organism:
Homo sapiens
Type:
Expression profiling by array
Platform:
GPL19171
6 Samples
Download data: CEL
Series
Accession:
GSE61266
ID:
200061266
17.

Genome-wide Definition of Promoter and Enhancer Usage During Neural Induction of Human Embryonic Stem Cells [ChIP-seq]

(Submitter supplied) Genome-wide mapping of transcriptional regulatory elements are essential tools for the understanding of the molecular events orchestrating self-renewal, commitment and differentiation of stem cells. We combined high-throughput identification of nascent, Pol-II-transcribed RNAs by Cap Analysis of Gene Expression (CAGE-Seq) with genome-wide profiling of histones modifications by chromatin immunoprecipitation (ChIP-seq) to map active promoters and enhancers in a model of human neural commitment, represented by embryonic stem cells (ESCs) induced to differentiate into self-renewing neuroepithelial-like stem cells (NESC). more...
Organism:
Homo sapiens
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL10999
3 Samples
Download data: BED
Series
Accession:
GSE61265
ID:
200061265
18.

Genome-wide Definition of Promoter and Enhancer Usage During Neural Induction of Human Embryonic Stem Cells [CAGE-seq]

(Submitter supplied) Genome-wide mapping of transcriptional regulatory elements are essential tools for the understanding of the molecular events orchestrating self-renewal, commitment and differentiation of stem cells. We combined high-throughput identification of nascent, Pol-II-transcribed RNAs by Cap Analysis of Gene Expression (CAGE-Seq) with genome-wide profiling of histones modifications by chromatin immunoprecipitation (ChIP-seq) to map active promoters and enhancers in a model of human neural commitment, represented by embryonic stem cells (ESCs) induced to differentiate into self-renewing neuroepithelial-like stem cells (NESC). more...
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platform:
GPL10999
1 Sample
Download data: TXT
Series
Accession:
GSE61264
ID:
200061264
19.

Jarid1b targets genes regulating development and is involved in neural differentiation

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Mus musculus
Type:
Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by array
Platforms:
GPL9185 GPL11078
16 Samples
Download data: BED, CEL
Series
Accession:
GSE31968
ID:
200031968
20.

Jarid1b targets genes regulating development and is involved in neural differentiation [expression array]

(Submitter supplied) The H3K4me2/3 histone demethylase Jarid1b (Kdm5b/Plu1) is dispensable for embryonic stem cell (ESC) self-renewal, but essential for ESC differentiation along the neural lineage. During neural differentiation, Jarid1b depleted ESCs fail to efficiently silence lineage-inappropriate genes, specifically stem and germ cell genes. Our results delineate an essential role for Jarid1b-mediated transcriptional control during ESC differentiation.
Organism:
Mus musculus
Type:
Expression profiling by array
Platform:
GPL11078
12 Samples
Download data: CEL
Series
Accession:
GSE31967
ID:
200031967
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